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Package 368/609HostnameOS / ArchBUILDCHECKBUILD BIN
MEDIPS 1.8.0
Lukas Chavez
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/MEDIPS
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: MEDIPS
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MEDIPS_1.8.0.tar.gz
StartedAt: 2013-03-25 00:20:16 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 00:30:46 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 630.0 seconds
RetCode: 0
Status:  OK 
CheckDir: MEDIPS.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/MEDIPS.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MEDIPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDIPS' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'MEDIPS' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 47.7Mb
  sub-directories of 1Mb or more:
    extdata  47.0Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
MEDIPS.CpGenrich           132.884 23.391 164.401
MEDIPS.selectSignificants  101.110  7.459 110.986
MEDIPS.plotSaturation       48.686  2.373  51.450
MEDIPS.saturationAnalysis   47.688  2.267  50.820
MEDIPS.plotCoverage         12.351  4.944  17.709
MEDIPS.coverageAnalysis     11.168  5.425  17.587
MEDIPS.methylProfiling       8.463  2.415  11.430
MEDIPS.plotCalibrationPlot   8.246  2.131  10.771
MEDIPS.normalize             6.530  2.242   9.194
MEDIPS.calibrationCurve      5.698  2.272   8.369
MEDIPS.exportWIG             5.001  1.500   6.689
MEDIPS.couplingVector        4.623  1.714   6.879
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/MEDIPS.Rcheck/00check.log'
for details.

MEDIPS.Rcheck/00install.out:

* installing *source* package 'MEDIPS' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c annotate.c -o annotate.o
annotate.c: In function 'annotate':
annotate.c:21: warning: suggest parentheses around comparison in operand of &
annotate.c:32: warning: suggest parentheses around comparison in operand of &
annotate.c:43: warning: suggest parentheses around comparison in operand of &
annotate.c:8: warning: unused variable 'rj'
annotate.c:8: warning: unused variable 'aj'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c calibration.c -o calibration.o
calibration.c: In function 'calibration':
calibration.c:10: warning: suggest parentheses around comparison in operand of &
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c coupling.c -o coupling.o
coupling.c: In function 'coupling':
coupling.c:26: warning: statement with no effect
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c profile.c -o profile.o
profile.c: In function 'profile':
profile.c:42: warning: unused variable 'wie'
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:34: warning: unused variable 'items'
profile.c:11: warning: unused variable 'pvalue'
profile.c:11: warning: unused variable 'Val'
profile.c:25: warning: 'ptrgenome_norm2' may be used uninitialized in this function
profile.c:25: warning: 'ptrgenome_raw2' may be used uninitialized in this function
profile.c:13: warning: 'ptr_input' may be used uninitialized in this function
profile.c:11: warning: 'nY' may be used uninitialized in this function
profile.c:11: warning: 'Y' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c roiprofile.c -o roiprofile.o
roiprofile.c: In function 'calculate':
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:12: warning: unused variable 'Val'
roiprofile.c: In function 'roiprofile':
roiprofile.c:280: warning: suggest parentheses around comparison in operand of &
roiprofile.c:282: warning: suggest parentheses around comparison in operand of &
roiprofile.c:294: warning: suggest parentheses around comparison in operand of &
roiprofile.c:296: warning: suggest parentheses around comparison in operand of &
roiprofile.c:248: warning: unused variable 'nProtected'
roiprofile.c: In function 'calculate':
roiprofile.c:29: warning: 'ptrinput' may be used uninitialized in this function
roiprofile.c:29: warning: 'IN' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o MEDIPS.so annotate.o calibration.o coupling.o profile.o roiprofile.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/MEDIPS.Rcheck/MEDIPS/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'MEDIPS.Rnw' 
** testing if installed package can be loaded

* DONE (MEDIPS)

MEDIPS.Rcheck/MEDIPS-Ex.timings:

nameusersystemelapsed
MEDIPS.CpGenrich132.884 23.391164.401
MEDIPS.annotate0.0400.0070.049
MEDIPS.calibrationCurve5.6982.2728.369
MEDIPS.couplingVector4.6231.7146.879
MEDIPS.coverageAnalysis11.168 5.42517.587
MEDIPS.exportWIG5.0011.5006.689
MEDIPS.genomeVector3.3391.1854.685
MEDIPS.getPositions3.0390.6993.843
MEDIPS.mergeFrames0.0060.0000.007
MEDIPS.methylProfiling 8.463 2.41511.430
MEDIPS.normalize6.5302.2429.194
MEDIPS.plotCalibrationPlot 8.246 2.13110.771
MEDIPS.plotCoverage12.351 4.94417.709
MEDIPS.plotSaturation48.686 2.37351.450
MEDIPS.readAlignedSequences1.8350.3632.393
MEDIPS.saturationAnalysis47.688 2.26750.820
MEDIPS.selectSignificants101.110 7.459110.986
MEDIPSset-class0.0010.0010.002